(to be clear, I know there are similar questions such as "How can I remap windows and alt keys in OS X?" - I'm not asking that. I can make the changes I want, they just get reset every time I unplug the keyboard)
So: Mac OS 10.6.5 on a MacBook Pro, with a Microsoft Natural Ergonomic Keyboard 4000 plugged in via a USB hub, along with other peripherals.
I want to switch the Alt and Windows keys, so their positions match that on the MBP's keyboard (Win key works as Command key with the Mac).
Sys Prefs / Keyboard / Modifier Keys does the job, until I unplug things to work elsewhere. Come back, plug the USB hub in as before, and my Option/Command swap has been forgotten.
Any suggestions as to how to get Mac OS to remember the swap?
The problem has vanished for me under OS X Lion. Same hardware, same hub, all of the modifiers are remembered.